22-20600473-A-G

Variant names:

• chr22-20600473-A-G
• rs165626

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.794 in 151,966 control chromosomes in the GnomAD database, including 48,194 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (48194 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120518 AN: 151848 Hom.: 48140 Cov.: 30

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.818

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.794 AC: 120626 AN: 151966 Hom.: 48194 Cov.: 30 AF XY: 0.796 AC XY: 59148 AN XY: 74278

African (AFR) AF: 0.866 AC: 35886 AN: 41446

American (AMR) AF: 0.823 AC: 12581 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2470 AN: 3466

East Asian (EAS) AF: 0.960 AC: 4957 AN: 5162

South Asian (SAS) AF: 0.788 AC: 3781 AN: 4798

European-Finnish (FIN) AF: 0.777 AC: 8234 AN: 10594

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50073 AN: 67908

Other (OTH) AF: 0.819 AC: 1729 AN: 2110

Alfa AF: 0.762 Hom.: 142052

Bravo AF: 0.801

Asia WGS AF: 0.879 AC: 3058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		-0.010

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs165626; hg19: chr22-20954760;